OpenRaiser/Intern-Atlas huggingface dataset:
MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models
Venue: arXiv cs.LG 2025
Year: 2025

Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this, several generative models have been proposed to generate surrogate trajectories at lower cost. Yet, these models typically learn a fixed-lag transition density, causing the training signal to be dominated by frequent but uninformative transitions. We introduce a new class of generative models, MSM Emulators, which instead learn to sample transitions across discrete states defined by an underlying Markov State Model (MSM). We instantiate this class with Markov Space Flow Matching (MarS-FM), whose sampling offers more than two orders of magnitude speedup compared to implicit- or explicit-solvent MD simulations. We benchmark Mars-FM ability to reproduce MD statistics through structural observables such as RMSD, radius of gyration, and secondary structure content. Our evaluation spans protein domains (up to 500 residues) with significant chemical and structural diversity, including unfolding events, and enforces strict sequence dissimilarity between training and test sets to assess generalization. Across all metrics, MarS-FM outperforms existing methods, often by a substantial margin.
Sparse Autoencoders Make Audio Foundation Models more Explainable
Venue: arXiv cs.SD 2025
Year: 2025

Audio pretrained models are widely employed to solve various tasks in speech processing, sound event detection, or music information retrieval. However, the representations learned by these models are unclear, and their analysis mainly restricts to linear probing of the hidden representations. In this work, we explore the use of Sparse Autoencoders (SAEs) to analyze the hidden representations of pretrained models, focusing on a case study in singing technique classification. We first demonstrate that SAEs retain both information about the original representations and class labels, enabling their internal structure to provide insights into self-supervised learning systems. Furthermore, we show that SAEs enhance the disentanglement of vocal attributes, establishing them as an effective tool for identifying the underlying factors encoded in the representations.
KnowGuard: Knowledge-Driven Abstention for Multi-Round Clinical Reasoning
Venue: arXiv cs.CL 2025
Year: 2025

In clinical practice, physicians refrain from making decisions when patient information is insufficient. This behavior, known as abstention, is a critical safety mechanism preventing potentially harmful misdiagnoses. Recent investigations have reported the application of large language models (LLMs) in medical scenarios. However, existing LLMs struggle with the abstentions, frequently providing overconfident responses despite incomplete information. This limitation stems from conventional abstention methods relying solely on model self-assessments, which lack systematic strategies to identify knowledge boundaries with external medical evidences. To address this, we propose \textbf{KnowGuard}, a novel \textit{investigate-before-abstain} paradigm that integrates systematic knowledge graph exploration for clinical decision-making. Our approach consists of two key stages operating on a shared contextualized evidence pool: 1) an evidence discovery stage that systematically explores the medical knowledge space through graph expansion and direct retrieval, and 2) an evidence evaluation stage that ranks evidence using multiple factors to adapt exploration based on patient context and conversation history. This two-stage approach enables systematic knowledge graph exploration, allowing models to trace structured reasoning paths and recognize insufficient medical evidence. We evaluate our abstention approach using open-ended multi-round clinical benchmarks that mimic realistic diagnostic scenarios, assessing abstention quality through accuracy-efficiency trade-offs beyond existing closed-form evaluations. Experimental evidences clearly demonstrate that KnowGuard outperforms state-of-the-art abstention approaches, improving diagnostic accuracy by 3.93\% while reducing unnecessary interaction by 7.27 turns on average.
Of-SemWat: High-payload text embedding for semantic watermarking of AI-generated images with arbitrary size
Venue: arXiv cs.CR 2025
Year: 2025

We propose a high-payload image watermarking method for textual embedding, where a semantic description of the image - which may also correspond to the input text prompt-, is embedded inside the image. In order to be able to robustly embed high payloads in large-scale images - such as those produced by modern AI generators - the proposed approach builds upon a traditional watermarking scheme that exploits orthogonal and turbo codes for improved robustness, and integrates frequency-domain embedding and perceptual masking techniques to enhance watermark imperceptibility. Experiments show that the proposed method is extremely robust against a wide variety of image processing, and the embedded text can be retrieved also after traditional and AI inpainting, permitting to unveil the semantic modification the image has undergone via image-text mismatch analysis.
PredNext: Explicit Cross-View Temporal Prediction for Unsupervised Learning in Spiking Neural Networks
Venue: arXiv cs.NE 2025
Year: 2025

Spiking Neural Networks (SNNs), with their temporal processing capabilities and biologically plausible dynamics, offer a natural platform for unsupervised representation learning. However, current unsupervised SNNs predominantly employ shallow architectures or localized plasticity rules, limiting their ability to model long-range temporal dependencies and maintain temporal feature consistency. This results in semantically unstable representations, thereby impeding the development of deep unsupervised SNNs for large-scale temporal video data. We propose PredNext, which explicitly models temporal relationships through cross-view future Step Prediction and Clip Prediction. This plug-and-play module seamlessly integrates with diverse self-supervised objectives. We firstly establish standard benchmarks for SNN self-supervised learning on UCF101, HMDB51, and MiniKinetics, which are substantially larger than conventional DVS datasets. PredNext delivers significant performance improvements across different tasks and self-supervised methods. PredNext achieves performance comparable to ImageNet-pretrained supervised weights through unsupervised training solely on UCF101. Additional experiments demonstrate that PredNext, distinct from forced consistency constraints, substantially improves temporal feature consistency while enhancing network generalization capabilities. This work provides a effective foundation for unsupervised deep SNNs on large-scale temporal video data.
PhysicsMinions: Winning Gold Medals in the Latest Physics Olympiads with a Coevolutionary Multimodal Multi-Agent System
Venue: arXiv cs.AI 2025
Year: 2025

Physics is central to understanding and shaping the real world, and the ability to solve physics problems is a key indicator of real-world physical intelligence. Physics Olympiads, renowned as the crown of competitive physics, provide a rigorous testbed requiring complex reasoning and deep multimodal understanding, yet they remain largely underexplored in AI research. Existing approaches are predominantly single-model based, and open-source MLLMs rarely reach gold-medal-level performance. To address this gap, we propose PhysicsMinions, a coevolutionary multi-agent system for Physics Olympiad. Its architecture features three synergistic studios: a Visual Studio to interpret diagrams, a Logic Studio to formulate solutions, and a Review Studio to perform dual-stage verification. The system coevolves through an iterative refinement loop where feedback from the Review Studio continuously guides the Logic Studio, enabling the system to self-correct and converge towards the ground truth. Evaluated on the HiPhO benchmark spanning 7 latest physics Olympiads, PhysicsMinions delivers three major breakthroughs: (i) Strong generalization: it consistently improves both open-source and closed-source models of different sizes, delivering clear benefits over their single-model baselines; (ii) Historic breakthroughs: it elevates open-source models from only 1-2 to 6 gold medals across 7 Olympiads, achieving the first-ever open-source gold medal in the latest International Physics Olympiad (IPhO) under the average-score metric; and (iii) Scaling to human expert: it further advances the open-source Pass@32 score to 26.8/30 points on the latest IPhO, ranking 4th of 406 contestants and far surpassing the top single-model score of 22.7 (ranked 22nd). Generally, PhysicsMinions offers a generalizable framework for Olympiad-level problem solving, with the potential to extend across disciplines.
MMRQA: Signal-Enhanced Multimodal Large Language Models for MRI Quality Assessment
Venue: arXiv cs.CV 2025
Year: 2025

Magnetic resonance imaging (MRI) quality assessment is crucial for clinical decision-making, yet remains challenging due to data scarcity and protocol variability. Traditional approaches face fundamental trade-offs: signal-based methods like MRIQC provide quantitative metrics but lack semantic understanding, while deep learning approaches achieve high accuracy but sacrifice interpretability. To address these limitations, we introduce the Multimodal MRI Quality Assessment (MMRQA) framework, pioneering the integration of multimodal large language models (MLLMs) with acquisition-aware signal processing. MMRQA combines three key innovations: robust metric extraction via MRQy augmented with simulated artifacts, structured transformation of metrics into question-answer pairs using Qwen, and parameter-efficient fusion through Low-Rank Adaptation (LoRA) of LLaVA-OneVision. Evaluated on MR-ART, FastMRI, and MyConnectome benchmarks, MMRQA achieves state-of-the-art performance with strong zero-shot generalization, as validated by comprehensive ablation studies. By bridging quantitative analysis with semantic reasoning, our framework generates clinically interpretable outputs that enhance quality control in dynamic medical settings.
HBSplat: Robust Sparse-View Gaussian Reconstruction with Hybrid-Loss Guided Depth and Bidirectional Warping
Venue: arXiv cs.CV 2025
Year: 2025

Novel View Synthesis (NVS) from sparse views presents a formidable challenge in 3D reconstruction, where limited multi-view constraints lead to severe overfitting, geometric distortion, and fragmented scenes. While 3D Gaussian Splatting (3DGS) delivers real-time, high-fidelity rendering, its performance drastically deteriorates under sparse inputs, plagued by floating artifacts and structural failures. To address these challenges, we introduce HBSplat, a unified framework that elevates 3DGS by seamlessly integrating robust structural cues, virtual view constraints, and occluded region completion. Our core contributions are threefold: a Hybrid-Loss Depth Estimation module that ensures multi-view consistency by leveraging dense matching priors and integrating reprojection, point propagation, and smoothness constraints; a Bidirectional Warping Virtual View Synthesis method that enforces substantially stronger constraints by creating high-fidelity virtual views through bidirectional depth-image warping and multi-view fusion; and an Occlusion-Aware Reconstruction component that recovers occluded areas using a depth-difference mask and a learning-based inpainting model. Extensive evaluations on LLFF, Blender, and DTU benchmarks validate that HBSplat sets a new state-of-the-art, achieving up to 21.13 dB PSNR and 0.189 LPIPS, while maintaining real-time inference. Code is available at: https://github.com/eternalland/HBSplat.
DAM: Dual Active Learning with Multimodal Foundation Model for Source-Free Domain Adaptation
Venue: arXiv cs.CV 2025
Year: 2025

Source-free active domain adaptation (SFADA) enhances knowledge transfer from a source model to an unlabeled target domain using limited manual labels selected via active learning. While recent domain adaptation studies have introduced Vision-and-Language (ViL) models to improve pseudo-label quality or feature alignment, they often treat ViL-based and data supervision as separate sources, lacking effective fusion. To overcome this limitation, we propose Dual Active learning with Multimodal (DAM) foundation model, a novel framework that integrates multimodal supervision from a ViL model to complement sparse human annotations, thereby forming a dual supervisory signal. DAM initializes stable ViL-guided targets and employs a bidirectional distillation mechanism to foster mutual knowledge exchange between the target model and the dual supervisions during iterative adaptation. Extensive experiments demonstrate that DAM consistently outperforms existing methods and sets a new state-of-the-art across multiple SFADA benchmarks and active learning strategies.
RealUnify: Do Unified Models Truly Benefit from Unification? A Comprehensive Benchmark
Venue: arXiv cs.AI 2025
Year: 2025

The integration of visual understanding and generation into unified multimodal models represents a significant stride toward general-purpose AI. However, a fundamental question remains unanswered by existing benchmarks: does this architectural unification actually enable synergetic interaction between the constituent capabilities? Existing evaluation paradigms, which primarily assess understanding and generation in isolation, are insufficient for determining whether a unified model can leverage its understanding to enhance its generation, or use generative simulation to facilitate deeper comprehension. To address this critical gap, we introduce RealUnify, a benchmark specifically designed to evaluate bidirectional capability synergy. RealUnify comprises 1,000 meticulously human-annotated instances spanning 10 categories and 32 subtasks. It is structured around two core axes: 1) Understanding Enhances Generation, which requires reasoning (e.g., commonsense, logic) to guide image generation, and 2) Generation Enhances Understanding, which necessitates mental simulation or reconstruction (e.g., of transformed or disordered visual inputs) to solve reasoning tasks. A key contribution is our dual-evaluation protocol, which combines direct end-to-end assessment with a diagnostic stepwise evaluation that decomposes tasks into distinct understanding and generation phases. This protocol allows us to precisely discern whether performance bottlenecks stem from deficiencies in core abilities or from a failure to integrate them. Through large-scale evaluations of 12 leading unified models and 6 specialized baselines, we find that current unified models still struggle to achieve effective synergy, indicating that architectural unification alone is insufficient. These results highlight the need for new training strategies and inductive biases to fully unlock the potential of unified modeling.
Learning Goal-Oriented Language-Guided Navigation with Self-Improving Demonstrations at Scale
Venue: arXiv cs.CV 2025
Year: 2025

Goal-oriented language-guided navigation requires robust exploration capabilities for agents to navigate to specified goals in unknown environments without step-by-step instructions. Existing methods tend to exclusively utilize shortest-path trajectories, lacking effective exploration priors for training navigation agents. To address the above challenges, we present SID, a goal-oriented language-guided navigation learning approach with Self-Improving Demonstrations. Specifically, SID learns an initial agent on the shortest-path data sampled from environments and then leverages this agent to generate novel exploration trajectories. The novel rollouts provide demonstrations with stronger exploration strategies to train a better agent, which in turn produces higher-quality agent demonstrations for the next round of training. We show that this iterative self-improving pipeline readily scales to new environments, and the resulting demonstrations can be transferred across a variety of language-guided navigation tasks, elevating the performance ceiling in diverse goal-oriented navigation tasks. Extensive experiments demonstrate that SID significantly boosts the exploration capabilities and generalization of navigation agents. The resulting agent achieves new state-of-the-art performance on goal-oriented language-guided navigation tasks, including REVERIE, SOON, notably achieving a 50.9% success rate on the unseen validation splits of SOON, surpassing the prior leading approaches by a margin of 13.9%.
OAT-FM: Optimal Acceleration Transport for Improved Flow Matching
Venue: arXiv cs.LG 2025
Year: 2025

As a powerful technique in generative modeling, Flow Matching (FM) aims to learn velocity fields from noise to data, which is often explained and implemented as solving Optimal Transport (OT) problems. In this study, we bridge FM and the recent theory of Optimal Acceleration Transport (OAT), developing an improved FM method called OAT-FM and exploring its benefits in both theory and practice. In particular, we demonstrate that the straightening objective hidden in existing OT-based FM methods is mathematically equivalent to minimizing the physical action associated with acceleration defined by OAT. Accordingly, instead of enforcing constant velocity, OAT-FM optimizes the acceleration transport in the product space of sample and velocity, whose objective corresponds to a necessary and sufficient condition of flow straightness. An efficient algorithm is designed to achieve OAT-FM with low complexity. OAT-FM motivates a new two-phase FM paradigm: Given a generative model trained by an arbitrary FM method, whose velocity information has been relatively reliable, we can fine-tune and improve it via OAT-FM. This paradigm eliminates the risk of data distribution drift and the need to generate a large number of noise data pairs, which consistently improves model performance in various generative tasks. Code is available at: https://github.com/AngxiaoYue/OAT-FM
Learning Distinguishable Representations in Deep Q-Networks for Linear Transfer
Venue: arXiv cs.LG 2025
Year: 2025

Deep Reinforcement Learning (RL) has demonstrated success in solving complex sequential decision-making problems by integrating neural networks with the RL framework. However, training deep RL models poses several challenges, such as the need for extensive hyperparameter tuning and high computational costs. Transfer learning has emerged as a promising strategy to address these challenges by enabling the reuse of knowledge from previously learned tasks for new, related tasks. This avoids the need for retraining models entirely from scratch. A commonly used approach for transfer learning in RL is to leverage the internal representations learned by the neural network during training. Specifically, the activations from the last hidden layer can be viewed as refined state representations that encapsulate the essential features of the input. In this work, we investigate whether these representations can be used as input for training simpler models, such as linear function approximators, on new tasks. We observe that the representations learned by standard deep RL models can be highly correlated, which limits their effectiveness when used with linear function approximation. To mitigate this problem, we propose a novel deep Q-learning approach that introduces a regularization term to reduce positive correlations between feature representation of states. By leveraging these reduced correlated features, we enable more effective use of linear function approximation in transfer learning. Through experiments and ablation studies on standard RL benchmarks and MinAtar games, we demonstrate the efficacy of our approach in improving transfer learning performance and thereby reducing computational overhead.
SecInfer: Preventing Prompt Injection via Inference-time Scaling
Venue: arXiv cs.CR 2025
Year: 2025

Prompt injection attacks pose a pervasive threat to the security of Large Language Models (LLMs). State-of-the-art prevention-based defenses typically rely on fine-tuning an LLM to enhance its security, but they achieve limited effectiveness against strong attacks. In this work, we propose \emph{SecInfer}, a novel defense against prompt injection attacks built on \emph{inference-time scaling}, an emerging paradigm that boosts LLM capability by allocating more compute resources for reasoning during inference. SecInfer consists of two key steps: \emph{system-prompt-guided sampling}, which generates multiple responses for a given input by exploring diverse reasoning paths through a varied set of system prompts, and \emph{target-task-guided aggregation}, which selects the response most likely to accomplish the intended task. Extensive experiments show that, by leveraging additional compute at inference, SecInfer effectively mitigates both existing and adaptive prompt injection attacks, outperforming state-of-the-art defenses as well as existing inference-time scaling approaches.
Light-SQ: Structure-aware Shape Abstraction with Superquadrics for Generated Meshes
Venue: arXiv cs.GR 2025
Year: 2025

In user-generated-content (UGC) applications, non-expert users often rely on image-to-3D generative models to create 3D assets. In this context, primitive-based shape abstraction offers a promising solution for UGC scenarios by compressing high-resolution meshes into compact, editable representations. Towards this end, effective shape abstraction must therefore be structure-aware, characterized by low overlap between primitives, part-aware alignment, and primitive compactness. We present Light-SQ, a novel superquadric-based optimization framework that explicitly emphasizes structure-awareness from three aspects. (a) We introduce SDF carving to iteratively udpate the target signed distance field, discouraging overlap between primitives. (b) We propose a block-regrow-fill strategy guided by structure-aware volumetric decomposition, enabling structural partitioning to drive primitive placement. (c) We implement adaptive residual pruning based on SDF update history to surpress over-segmentation and ensure compact results. In addition, Light-SQ supports multiscale fitting, enabling localized refinement to preserve fine geometric details. To evaluate our method, we introduce 3DGen-Prim, a benchmark extending 3DGen-Bench with new metrics for both reconstruction quality and primitive-level editability. Extensive experiments demonstrate that Light-SQ enables efficient, high-fidelity, and editable shape abstraction with superquadrics for complex generated geometry, advancing the feasibility of 3D UGC creation.
Embedded Deep Learning for Bio-hybrid Plant Sensors to Detect Increased Heat and Ozone Levels
Venue: arXiv cs.ET 2025
Year: 2025

We present a bio-hybrid environmental sensor system that integrates natural plants and embedded deep learning for real-time, on-device detection of temperature and ozone level changes. Our system, based on the low-power PhytoNode platform, records electric differential potential signals from Hedera helix and processes them onboard using an embedded deep learning model. We demonstrate that our sensing device detects changes in temperature and ozone with good sensitivity of up to 0.98. Daily and inter-plant variability, as well as limited precision, could be mitigated by incorporating additional training data, which is readily integrable in our data-driven framework. Our approach also has potential to scale to new environmental factors and plant species. By integrating embedded deep learning onboard our biological sensing device, we offer a new, low-power solution for continuous environmental monitoring and potentially other fields of application.